2YPI

CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis.

Lolis, E.Petsko, G.A.

(1990) Biochemistry 29: 6619-6625


  • PubMed Abstract: 
  • The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a ...

    The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a final R factor of 0.18. The interactions between the inhibitor and enzyme have been analyzed. The inhibitor forms hydrogen bonds to the side chains of His 95 and Glu 165. The latter hydrogen bond confirms that Glu 165 is protonated upon PGA binding. The structure of the complexed enzyme has been compared to that of the unbound form of the enzyme, and conformational changes have been observed: the side chain of Glu 165 moves over 2 A and a 10-residue flexible loop moves over 7 A to close over the active site. Spectroscopic results of phosphoglycolic acid binding to triosephosphate isomerase that have been amassed over the years are also explained in structural terms. The implications for catalysis are noted.


    Related Citations: 
    • Structure of Yeast Triosephosphate Isomerase at 1.9-Angstroms Resolution
      Lolis, E.,Alber, T.,Davenport, R.C.,Rose, D.,Hartman, F.C.,Petsko, G.A.
      (1990) Biochemistry 29: 6609
    • On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
      Alber, T.,Banner, D.W.,Bloomer, A.C.,Petsko, G.A.,Phillips, D.,Rivers, P.S.,Wilson, I.A.
      (1981) Philos.Trans.R.Soc.London,Ser.B 293: 159
    • Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark)
      Alber, T.C.,Davenportjunior, R.C.,Giammona, D.A.,Lolis, E.,Petsko, G.A.,Ringe, D.
      (1987) Cold Spring Harbor Symp.Quant.Biol. 52: 603
    • Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
      Alber, T.,Hartman, F.C.,Johnson, R.M.,Petsko, G.A.,Tsernoglou, D.
      (1981) J.Biol.Chem. 256: 1356


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A, B
247Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: TPI1
EC: 5.3.1.1
Find proteins for P00942 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TPI1
Go to UniProtKB:  P00942
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download SDF File 
Download CCD File 
A, B
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PGAKi: 15000 nM BINDINGMOAD
PGAKi: 15000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.350α = 90.00
b = 83.970β = 99.70
c = 38.670γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance